Pupils having breakfast in Wrexham. Photograph: Christopher Thomond for the Guardian

Almost a third of children regularly go without breakfast before school and are more likely than classmates to be inactive, unfit and obese, research shows.

While 68% of pupils eat before leaving home, 32% do not. Of the latter, 25% only sometimes have a morning meal and 7% never have breakfast on school days, according to findings which have raised fresh concern about children's eating habits and general health.

The study of 4,326 children, aged 10-16, in England was reported in the European Journal of Clinical Nutrition and found that 26.6% of boys and 38.6% of girls skipped breakfast some or all of the time. Boys often blame lack of time, while many girls missed breakfast because they believe doing so would help them lose weight.

"We found that children who skip breakfast either occasionally or routinely are less fit, less active and more likely to be overweight or obese than those who always eat breakfast," said lead author Dr Gavin Sandercock, a lecturer in clinical physiology at the University of Essex. "Children with the healthiest weight were always those who regularly had breakfast before heading to school.

"These findings are worrying because we found more obesity and lower levels of physical activity among skippers, which is of great concern because these children are more likely to develop chronic disease in adulthood like cancer, heart disease and diabetes," added Sandercock.

While girls who skipped breakfast are 92% more likely to become obese than female classmates who regularly eat before school, the equivalent figure in boys was 62%. But the boys were much likelier than female ones to have a sedentary lifestyle and, critically, have poor cardiorespiratory (heart and lung) fitness – the best predictor of chronic illness in later life, said Sandercock.

Until now it has been thought that children who missed breakfast were more likely to be obese because they snacked during the day and ate late at night. But the study suggests that their inactive lifestyles may also play a key role.

"This research should concern parents because they are putting their children at a higher risk of being overweight unless they make sure they eat breakfast before leaving the house, and are also increasing their risk of being unfit and inactive," said Sandercock. "It's of great concern that 32% of parents don't do that, especially as we already know that kids' concentration and ability to learn is worse when they miss breakfast."

Professor Mitch Blair of the Royal College of Paediatrics and Child Health said: "This is yet another study that reinforces the need for regular mealtime routines. We know that children model their behaviour on their parents and it would be interesting if the parents of the children in this study had similar habits."

Tam Fry, founder of the Child Growth Foundation and spokesman for the National Obesity Forum, said the study underlined the importance of breakfast for everyone. "Although 68% of the children studied always ate breakfast, there are areas of the country where, tragically, very few are given breakfast at home. That is why breakfast clubs at school are hugely important for them – not only for their physical fitness but also for their fitness to learn," said Fry.

But Sandercock said that while breakfast clubs are a good idea, they take away from parents the responsibility of preparing food for their offspring.

The most recent NHS figures show that 22.8% of children in England starting reception year at primary school at the age of four are overweight or obese, rising to 32.6% by the time they reach year six, the last year of primary school. Previous research has also shown that children's fitness is declining worldwide, including in those who are at normal weight, and is going down faster in England than the national average.